Algorithm for Sequence Analysis in Bioinformatics |
An intermediate level course on algorithms in bioinformatics. We will use it to explain common concepts in sequence analysis, starting from the biological relevance of sequence alignment and making our way through the most commonly used algorithms, including Needleman and Wunsch, Smith and Waterman for pairwise alignments, BLAST for database searches, Nussinov for RNA folding and the progressive multiple alignment. The practicals will be in Python and will involve driving the students through an implementation of these algorithms. The biobliography is given by order of importance. |
Practicals will be in python 2.7. They will involve adapting existing scripts rather than programming from scratch. For this reason, students with no practical knowledge of python but with a good grasp of programming languages like Perl, C or JAVA should manage reasonnably well. Students are expected to bring their own lap-top and advised to have a LINUX boot though Virtual MAchine support will be provided. |
| Date | Location | Session | Title | Links | |
| 14/01/20 - 17:30 | ASAB | LECTURE | 1-Pairwise comparisons in an evolutionary context | L | |
| 17/01/20 - 15:00 | ASAB | LECTURE | 2-Substitution Matrices | L | |
| 24/01/20 - 15:00 | ASAB | LECTURE | 3-Introduction to Dynamic Programming-1 | L | |
| 31/01/20 - 15:00 | ASAB | LECTURE | 4-Introduction to Dynamic Programming-2 | L | |
| 07/02/20 - 15:00 | ASAB | LECTURE | Mid Term Exam | ||
| 14/02/20 - 15:00 | ASAB | LECTURE | 5-Blast Algorithm | L | |
| 21/02/20 - 15:00 | ASAB | LECTURE | 6-Introduction to Multiple Sequence Alignment | L | |
| 28/02/20 - 15:00 | ASAB | LECTURE | 7-Multiple Sequence Alignment Algorithms | L | |
| 06/03/20 - 15:00 | ASAB | LECTURE | 8-RNA Folding Algorithms | L | |
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| 21/01/20 - 17:30 | ASAB | PRACTICALS | 1-Parsing Biological Files | P | |
| 28/01/20 - 17:30 | ASAB | PRACTICALS | 2-Computing Substitution Matrices | P | |
| 04/02/20 - 17:30 | ASAB | PRACTICALS | 3-Introduction to Dynamic Programming 1 | P | |
| 11/02/20 - 17:30 | ASAB | PRACTICALS | 4-Introduction to Dynamic Programming 2 | P | |
| 18/02/20 - 17:30 | ASAB | PRACTICALS | 5-Parsing and manipulating binary trees | P | |
| 25/02/20 - 17:30 | ASAB | PRACTICALS | 6-Implementing your own multiple sequence aligner | P | |
| 03/03/20 - 17:30 | ASAB | PRACTICALS | 7-Project Preparation | P | |
| 10/03/20 - 17:30 | ASAB | PRACTICALS | 8-Project Presentation | P | |
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This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available on request Cedric Notredame |